[R] distances between points in R^3

baptiste Auguié ba208 at exeter.ac.uk
Sun Feb 3 19:55:30 CET 2008

Dear R helpers,

I'm trying to write a numerical scheme for a boundary integral method  
to solve an electromagnetic problem. This requires the computation of  
the distance between points at the surface of an object (a sphere, in  
my example). Here is my code,

> require(rgl)
> r<-1
> size<-10
> theta<-seq(0,2*pi,length=size*2)
> phi<-seq(0,pi,length=size)
> pc = as.matrix(rbind(expand.grid(theta,phi)))
> x<- r* sin(pc[,2]) * cos(pc[,1])
> y<- r* sin(pc[,2]) * sin(pc[,1])
> z<- r* cos(pc[,2])
>   plot3d(x, y, z, col=rainbow(1000), size=2,zlim=c(-1,1)) #  
> scatterplot of points on a sphere
> df<- unique(rbind(x,y,z), MARGIN = 2 ) # removes duplicates in  
> cartesian coordinates
> dimension <- dim(df)[1]
> matDistances <- array(data=0,dim=c(dimension,dimension))
> norm <- function(a) sqrt(a %*% a)
> for (ii in 1:dimension){
> for (jj in ii:dimension){
> matDistances[ii,jj]<- norm( df[,ii] - df[,jj])
> }
> }

This is both inefficient and ugly, I'll welcome any suggestion. In  

- the location of the points on the sphere is not ideal (understand:  
not uniformly distributed over the area): i looked into delaunayn  
from the geometry package and qhull.com but at best I obtained a  
random set of points on the sphere. It must be a most classical  
problem –– generating a uniform distribution of points on a sphere––,  
but i've set that problem aside for the moment.

- the double for loop over all the points cries out for a vectorized  
solution, but i can't really think of any.

Many thanks in advance,


Baptiste Auguié

Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,

Phone: +44 1392 264187


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